Package evaluation to test Pathogen on Julia 1.14.0-DEV.1455 (9d9110fde9*) started at 2026-01-01T17:57:07.159 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.68s ################################################################################ # Installation # Installing Pathogen... Resolving package versions... Installed InlineStrings ─────────────── v1.4.5 Installed AbstractTrees ─────────────── v0.4.5 Installed FillArrays ────────────────── v1.15.0 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed HypergeometricFunctions ───── v0.3.28 Installed AliasTables ───────────────── v1.1.3 Installed DataStructures ────────────── v0.18.22 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed OnlineStatsBase ───────────── v1.7.1 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed StatsBase ─────────────────── v0.33.21 Installed DataAPI ───────────────────── v1.16.0 Installed RecipesBase ───────────────── v1.3.4 Installed InvertedIndices ───────────── v1.3.1 Installed DataValueInterfaces ───────── v1.0.0 Installed StatsAPI ──────────────────── v1.8.0 Installed Statistics ────────────────── v1.11.1 Installed ProgressMeter ─────────────── v1.11.0 Installed PrecompileTools ───────────── v1.3.3 Installed SentinelArrays ────────────── v1.4.9 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed IrrationalConstants ───────── v0.2.6 Installed LogExpFunctions ───────────── v0.3.29 Installed StringManipulation ────────── v0.4.2 Installed QuadGK ────────────────────── v2.11.2 Installed Rmath ─────────────────────── v0.9.0 Installed PtrArrays ─────────────────── v1.3.0 Installed StatsFuns ─────────────────── v1.5.2 Installed Tables ────────────────────── v1.12.1 Installed PrettyTables ──────────────── v3.1.2 Installed Distributions ─────────────── v0.25.122 Installed DataFrames ────────────────── v1.8.1 Installed Reexport ──────────────────── v1.2.2 Installed Missings ──────────────────── v1.2.0 Installed PooledArrays ──────────────── v1.4.3 Installed Preferences ───────────────── v1.5.1 Installed SpecialFunctions ──────────── v2.6.1 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed Pathogen ──────────────────── v0.4.13 Installed LaTeXStrings ──────────────── v1.4.0 Installed PDMats ────────────────────── v0.11.35 Installed Crayons ───────────────────── v4.1.1 Installed DocStringExtensions ───────── v0.9.5 Installed OnlineStats ───────────────── v1.7.3 Installed SortingAlgorithms ─────────── v1.2.2 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [c8189ad9] + Pathogen v0.4.13 Updating `~/.julia/environments/v1.14/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [66dad0bd] + AliasTables v1.1.3 [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [a15396b6] + OnlineStats v1.7.3 [925886fa] + OnlineStatsBase v1.7.1 [bac558e1] + OrderedCollections v1.8.1 ⌃ [90014a1f] + PDMats v0.11.35 [c8189ad9] + Pathogen v0.4.13 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [08abe8d2] + PrettyTables v3.1.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.9 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.2 [892a3eda] + StringManipulation v0.4.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 8.71s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 Precompilation failed after 14.01s ################################################################################ # Testing # Testing Pathogen Status `/tmp/jl_R3hyEo/Project.toml` [a93c6f00] DataFrames v1.8.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [a15396b6] OnlineStats v1.7.3 [c8189ad9] Pathogen v0.4.13 [92933f4c] ProgressMeter v1.11.0 [3cdcf5f2] RecipesBase v1.3.4 [10745b16] Statistics v1.11.1 ⌅ [2913bbd2] StatsBase v0.33.21 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_R3hyEo/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [34da2185] Compat v4.18.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.15.0 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [a15396b6] OnlineStats v1.7.3 [925886fa] OnlineStatsBase v1.7.1 [bac558e1] OrderedCollections v1.8.1 ⌃ [90014a1f] PDMats v0.11.35 [c8189ad9] Pathogen v0.4.13 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [8e850b90] libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... WARNING: Constructor for type "UInt8" was extended in `Pathogen` without explicit qualification or import.  NOTE: Assumed "UInt8" refers to `Base.UInt8`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function UInt8 end`.  Hint: To silence the warning, qualify `UInt8` as `Base.UInt8` in the method signature or explicitly `import Base: UInt8`. WARNING: method definition for generate at /home/pkgeval/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:1 declares type variable T but does not use it. WARNING: method definition for generate at /home/pkgeval/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:20 declares type variable T but does not use it. WARNING: method definition for apply_recipe at /home/pkgeval/.julia/packages/RecipesBase/BRe07/src/RecipesBase.jl:296 declares type variable T but does not use it. WARNING: method definition for apply_recipe at /home/pkgeval/.julia/packages/RecipesBase/BRe07/src/RecipesBase.jl:296 declares type variable T but does not use it. WARNING: method definition for apply_recipe at /home/pkgeval/.julia/packages/RecipesBase/BRe07/src/RecipesBase.jl:296 declares type variable T but does not use it. 1 dependency had output during precompilation: ┌ Pathogen │ [Output was shown above] └ ┌ Warning: `Progress(n::Integer, desc::AbstractString, offset::Integer = 0; kwargs...)` is deprecated, use `Progress(n; desc = desc, offset = offset, kwargs...)` instead. │ caller = ip:0x0 └ @ Core :-1 Initialization progress 1%|▏ | ETA: 2:06:08 Initialization progress 100%|████████████████████████████| Time: 0:00:51 MCMC progress 1%|▎ | ETA: 1:44:04 MCMC progress 10%|███▊ | ETA: 0:06:18 MCMC progress 20%|███████▌ | ETA: 0:02:52 MCMC progress 29%|███████████▏ | ETA: 0:01:42 MCMC progress 38%|██████████████▋ | ETA: 0:01:08 MCMC progress 47%|█████████████████▊ | ETA: 0:00:49 MCMC progress 55%|█████████████████████ | ETA: 0:00:34 MCMC progress 64%|████████████████████████▎ | ETA: 0:00:24 MCMC progress 72%|███████████████████████████▎ | ETA: 0:00:17 MCMC progress 79%|██████████████████████████████▏ | ETA: 0:00:11 MCMC progress 87%|█████████████████████████████████▏ | ETA: 0:00:06 MCMC progress 95%|████████████████████████████████████▎ | ETA: 0:00:02 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:49 Initialization progress 2%|▌ | ETA: 0:00:31 Initialization progress 100%|████████████████████████████| Time: 0:00:00 MCMC progress 2%|▊ | ETA: 0:01:42 MCMC progress 21%|████████ | ETA: 0:00:08 MCMC progress 69%|██████████████████████████▎ | ETA: 0:00:01 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:02 Test Summary: | Pass Total Time SEIR Model | 89 89 2m32.9s Initialization progress 1%|▏ | ETA: 0:53:00 Initialization progress 29%|████████ | ETA: 0:00:53 Initialization progress 60%|████████████████▊ | ETA: 0:00:14 Initialization progress 91%|█████████████████████████▋ | ETA: 0:00:02 Initialization progress 100%|████████████████████████████| Time: 0:00:22 MCMC progress 1%|▎ | ETA: 0:45:14 MCMC progress 12%|████▋ | ETA: 0:02:10 MCMC progress 24%|█████████▎ | ETA: 0:00:57 MCMC progress 36%|█████████████▊ | ETA: 0:00:33 MCMC progress 48%|██████████████████▏ | ETA: 0:00:21 MCMC progress 60%|██████████████████████▊ | ETA: 0:00:13 MCMC progress 73%|███████████████████████████▊ | ETA: 0:00:07 MCMC progress 86%|████████████████████████████████▋ | ETA: 0:00:03 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:19 MCMC progress 21%|████████ | ETA: 0:00:00 MCMC progress 83%|███████████████████████████████▌ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SEI Model | 167 167 59.7s Initialization progress 1%|▏ | ETA: 0:56:19 Initialization progress 29%|████████ | ETA: 0:00:57 Initialization progress 58%|████████████████▍ | ETA: 0:00:16 Initialization progress 88%|████████████████████████▋ | ETA: 0:00:03 Initialization progress 100%|████████████████████████████| Time: 0:00:23 MCMC progress 1%|▎ | ETA: 0:45:47 MCMC progress 11%|████▎ | ETA: 0:02:25 MCMC progress 23%|████████▋ | ETA: 0:01:04 MCMC progress 34%|████████████▊ | ETA: 0:00:37 MCMC progress 44%|████████████████▉ | ETA: 0:00:24 MCMC progress 55%|████████████████████▉ | ETA: 0:00:16 MCMC progress 66%|█████████████████████████▏ | ETA: 0:00:10 MCMC progress 77%|█████████████████████████████▎ | ETA: 0:00:06 MCMC progress 87%|█████████████████████████████████ | ETA: 0:00:03 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:19 MCMC progress 18%|██████▉ | ETA: 0:00:00 MCMC progress 28%|██████████▋ | ETA: 0:00:02 MCMC progress 93%|███████████████████████████████████▍ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SIR Model | 170 170 1m02.6s Initialization progress 1%|▏ | ETA: 0:52:53 Initialization progress 32%|█████████ | ETA: 0:00:45 Initialization progress 65%|██████████████████▎ | ETA: 0:00:12 Initialization progress 100%|████████████████████████████| Time: 0:00:22 MCMC progress 1%|▎ | ETA: 0:40:22 MCMC progress 13%|████▉ | ETA: 0:01:53 MCMC progress 24%|█████████ | ETA: 0:00:53 MCMC progress 35%|█████████████▍ | ETA: 0:00:30 MCMC progress 47%|█████████████████▉ | ETA: 0:00:19 MCMC progress 59%|██████████████████████▍ | ETA: 0:00:12 MCMC progress 71%|███████████████████████████▏ | ETA: 0:00:07 MCMC progress 83%|███████████████████████████████▌ | ETA: 0:00:03 MCMC progress 95%|████████████████████████████████████ | ETA: 0:00:01 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:17 MCMC progress 2%|▊ | ETA: 0:00:08 MCMC progress 81%|██████████████████████████████▊ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SI Model | 106 106 56.5s Testing Pathogen tests passed Testing completed after 507.88s PkgEval succeeded after 757.62s